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   <h1 id="index">Index</h1>

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   <a href="#_"><strong>_</strong></a> | <a href="#A"><strong>A</strong></a> | <a href="#B"><strong>B</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#J"><strong>J</strong></a> | <a href="#K"><strong>K</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#N"><strong>N</strong></a> | <a href="#O"><strong>O</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#Q"><strong>Q</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a> | <a href="#U"><strong>U</strong></a> | <a href="#V"><strong>V</strong></a> | <a href="#W"><strong>W</strong></a> | <a href="#X"><strong>X</strong></a> 
   </div>
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter.__init__">__init__() (MDAnalysis.selections.base.SelectionWriter method)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._compressed_formats">_compressed_formats (in module MDAnalysis.coordinates.__init__)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._frame_writers">_frame_writers (in module MDAnalysis.coordinates.__init__)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._topology_coordinates_readers">_topology_coordinates_readers (in module MDAnalysis.coordinates.__init__)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._trajectory_readers">_trajectory_readers (in module MDAnalysis.coordinates.__init__)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._trajectory_readers_permissive">_trajectory_readers_permissive (in module MDAnalysis.coordinates.__init__)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#MDAnalysis.coordinates.__init__._trajectory_writers">_trajectory_writers (in module MDAnalysis.coordinates.__init__)</a></dt>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter._translate">_translate() (MDAnalysis.selections.base.SelectionWriter method)</a></dt>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter._write_head">_write_head() (MDAnalysis.selections.base.SelectionWriter method)</a></dt>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter._write_tail">_write_tail() (MDAnalysis.selections.base.SelectionWriter method)</a></dt>
</dl></td>
</tr></table>

<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.active_reader">active_reader (MDAnalysis.coordinates.base.ChainReader attribute)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection.addTimeseries">addTimeseries() (MDAnalysis.core.Timeseries.TimeseriesCollection method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.align_principalAxis">align_principalAxis() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.alignto">alignto() (in module MDAnalysis.analysis.align)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.all_get_indices">all_get_indices() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.all_get_radii">all_get_radii() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.all_search">all_search() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Angle">Angle (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.angle">angle() (in module MDAnalysis.core.util)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.angle">(MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.anyopen">anyopen() (in module MDAnalysis.core.util)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball">Arcball (class in MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.arcball_nearest_axis">arcball_nearest_axis() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.asiterable">asiterable() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.asUniverse">asUniverse() (in module MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom">Atom (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Atom">(class in MDAnalysis.core.Timeseries)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.ATOM">ATOM() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter.ATOM">(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/topology/tables.html#MDAnalysis.topology.tables.atomelements">atomelements (in module MDAnalysis.topology.tables)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup">AtomGroup (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch">AtomNeighborSearch (class in MDAnalysis.KDTree.NeighborSearch)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.atoms">atoms (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
</dl></td>
</tr></table>

<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.BackboneSelection">BackboneSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.BaseSelection">BaseSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bbox">bbox() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Bfactor2RMSF">Bfactor2RMSF() (in module MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.BfactorDensityCreator">BfactorDensityCreator (class in MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bfactors">bfactors (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Bond">Bond (class in MDAnalysis.core.Timeseries)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.Bond">(class in MDAnalysis.topology.core)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bond">bond() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.box_volume">box_volume() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.bsphere">bsphere() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.build_bondlists">build_bondlists() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.build_segments">build_segments() (in module MDAnalysis.topology.core)</a></dt>
</dl></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.calc_angle">calc_angle() (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis method)</a></dt>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.calc_eucl_distance">calc_eucl_distance() (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis method)</a></dt>
    <dt><a href="documentation_pages/core/qcprot.html#MDAnalysis.core.qcprot.CalcRMSDRotationalMatrix">CalcRMSDRotationalMatrix() (in module MDAnalysis.core.qcprot)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.CASelection">CASelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.CenterOfGeometry">CenterOfGeometry (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfGeometry">centerOfGeometry() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.CenterOfMass">CenterOfMass (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centerOfMass">centerOfMass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.centers">centers() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.centers">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.centroid">centroid() (MDAnalysis.core.AtomGroup.Atom method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.centroid">(MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader">ChainReader (class in MDAnalysis.coordinates.base)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.charges">charges() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.chargeUnit_factor">chargeUnit_factor (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.check_compatible">check_compatible() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.check_compatible">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection.clear">clear() (MDAnalysis.core.Timeseries.TimeseriesCollection method)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.clear_handlers">clear_handlers() (in module MDAnalysis.core.log)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.close">close() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader.close">(MDAnalysis.coordinates.TRJ.TRJReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XYZ.html#MDAnalysis.coordinates.XYZ.XYZReader.close">(MDAnalysis.coordinates.XYZ.XYZReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.close">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.close">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.close_trajectory">close_trajectory() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.close_trajectory">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.close_trajectory">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.close_trajectory">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.close_trajectory">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter.comment">comment() (MDAnalysis.selections.base.SelectionWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/selections/charmm.html#MDAnalysis.selections.charmm.SelectionWriter.comment">(MDAnalysis.selections.charmm.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/gromacs.html#MDAnalysis.selections.gromacs.SelectionWriter.comment">(MDAnalysis.selections.gromacs.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/pymol.html#MDAnalysis.selections.pymol.SelectionWriter.comment">(MDAnalysis.selections.pymol.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/vmd.html#MDAnalysis.selections.vmd.SelectionWriter.comment">(MDAnalysis.selections.vmd.SelectionWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.compose_matrix">compose_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection.compute">compute() (MDAnalysis.core.Timeseries.TimeseriesCollection method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.concatenate_matrices">concatenate_matrices() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/analysis/distances.html#MDAnalysis.analysis.distances.contact_matrix">contact_matrix() (in module MDAnalysis.analysis.distances)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis">ContactAnalysis (class in MDAnalysis.analysis.contacts)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1">ContactAnalysis1 (class in MDAnalysis.analysis.contacts)</a>, <a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1">[1]</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.ContactAnalysis1">ContactAnalysis1.ContactAnalysis1 (class in MDAnalysis.analysis.contacts)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.plot">ContactAnalysis1.plot() (in module MDAnalysis.analysis.contacts)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg">ContactAnalysis1.plot_qavg() (in module MDAnalysis.analysis.contacts)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.conversion_factor">conversion_factor (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.convert">convert() (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.convert_aa_code">convert_aa_code() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.convert_density">convert_density() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.convert_dimensions_to_unitcell">convert_dimensions_to_unitcell() (MDAnalysis.coordinates.base.Writer method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/GRO.html#MDAnalysis.coordinates.GRO.GROWriter.convert_dimensions_to_unitcell">(MDAnalysis.coordinates.GRO.GROWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_dimensions_to_unitcell">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_dimensions_to_unitcell">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.convert_length">convert_length() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_pos_from_native">convert_pos_from_native() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_from_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_from_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_from_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_from_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_pos_to_native">convert_pos_to_native() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_pos_to_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_pos_to_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_pos_to_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_pos_to_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_time_from_native">convert_time_from_native() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_from_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_from_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_from_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_from_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.convert_time_to_native">convert_time_to_native() (MDAnalysis.coordinates.base.IObase method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.convert_time_to_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.convert_time_to_native">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.convert_time_to_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.convert_time_to_native">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.coord">coord (MDAnalysis.core.AtomGroup.Universe attribute)</a></dt>
    <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch">CoordinateNeighborSearch (class in MDAnalysis.KDTree.NeighborSearch)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.coordinates">coordinates() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.correl">correl() (MDAnalysis.coordinates.DCD.DCDReader method)</a></dt>
    <dt><a href="documentation_pages/coordinates/CRD.html#MDAnalysis.coordinates.CRD.CRDReader">CRDReader (class in MDAnalysis.coordinates.CRD)</a></dt>
    <dt><a href="documentation_pages/coordinates/CRD.html#MDAnalysis.coordinates.CRD.CRDWriter">CRDWriter (class in MDAnalysis.coordinates.CRD)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.create">create() (in module MDAnalysis.core.log)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.CRYST1">CRYST1() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter.CRYST1">(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader">DCDReader (class in MDAnalysis.coordinates.DCD)</a></dt>
    <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter">DCDWriter (class in MDAnalysis.coordinates.DCD)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.decompose_matrix">decompose_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.DEFAULT_ACCEPTORS">DEFAULT_ACCEPTORS (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis attribute)</a></dt>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.DEFAULT_DONORS">DEFAULT_DONORS (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis attribute)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.delta">delta (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.delta">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density">Density (class in MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.BfactorDensityCreator.Density">Density() (MDAnalysis.analysis.density.BfactorDensityCreator method)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.density_from_PDB">density_from_PDB() (in module MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.density_from_trajectory">density_from_trajectory() (in module MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.density_from_Universe">density_from_Universe() (in module MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.densityUnit_factor">densityUnit_factor (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Dihedral">Dihedral (class in MDAnalysis.core.Timeseries)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dihedral">dihedral() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dihedral_numpy">dihedral_numpy() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dihedral_orig">dihedral_orig() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.DIM">DIM (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.dimensions">dimensions (MDAnalysis.coordinates.base.Timestep attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.Timestep.dimensions">(MDAnalysis.coordinates.TRJ.Timestep attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.dimensions">(MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.dimensions">(MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)</a></dt>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.dimensions">(MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.dimensions">(MDAnalysis.core.AtomGroup.Universe attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/distances.html#MDAnalysis.analysis.distances.dist">dist() (in module MDAnalysis.analysis.distances)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Distance">Distance (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/analysis/distances.html#MDAnalysis.analysis.distances.distance_array">distance_array() (in module MDAnalysis.analysis.distances)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/distances.html#MDAnalysis.core.distances.distance_array">(in module MDAnalysis.core.distances)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flags.doc">doc() (MDAnalysis.core.__init__.Flags method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.down">down() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.drag">drag() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.dt">dt (MDAnalysis.coordinates.base.Reader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.dt">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.dt">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.echo">echo() (in module MDAnalysis.core.log)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.ProgressMeter.echo">(MDAnalysis.core.log.ProgressMeter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.euler_from_quaternion">euler_from_quaternion() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.exdrCLOSE">exdrCLOSE (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.exdrENDOFFILE">exdrENDOFFILE (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.exdrFILENOTFOUND">exdrFILENOTFOUND (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.exdrOK">exdrOK (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.export">export() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.export">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.fasta2select">fasta2select() (in module MDAnalysis.analysis.align)</a></dt>
    <dt><a href="documentation_pages/core/qcprot.html#MDAnalysis.core.qcprot.FastCalcRMSDAndRotation">FastCalcRMSDAndRotation() (in module MDAnalysis.core.qcprot)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.filename">filename() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.fixedwidth_bins">fixedwidth_bins() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flag">Flag (class in MDAnalysis.core.__init__)</a></dt>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flags">Flags (class in MDAnalysis.core.__init__)</a></dt>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.flags">flags (in module MDAnalysis.core.__init__)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.flagsDocs">flagsDocs (class in MDAnalysis.core.__init__)</a></dt>
    <dt><a href="documentation_pages/coordinates/GRO.html#MDAnalysis.coordinates.GRO.GROWriter.fmt">fmt (MDAnalysis.coordinates.GRO.GROWriter attribute)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.format">format (MDAnalysis.coordinates.base.IObase attribute)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.FORTRAN_format_regex">FORTRAN_format_regex (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.FORTRANReader">FORTRANReader (class in MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.frame">frame (MDAnalysis.coordinates.base.ChainReader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.frame">(MDAnalysis.coordinates.base.Reader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.frame">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.frame">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.generate_table">generate_table() (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis method)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.get_atom_mass">get_atom_mass() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PDBReader.get_bfactors">get_bfactors() (MDAnalysis.coordinates.PDB.PDBReader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_bfactors">(MDAnalysis.coordinates.PDB.PrimitivePDBReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_bfactors">(MDAnalysis.coordinates.PDBQT.PDBQTReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader.get_charges">get_charges() (MDAnalysis.coordinates.PQR.PQRReader method)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.get_conversion_factor">get_conversion_factor() (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.get_indices">get_indices() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader.get_occupancy">get_occupancy() (MDAnalysis.coordinates.PDB.PrimitivePDBReader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader.get_occupancy">(MDAnalysis.coordinates.PDBQT.PDBQTReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.get_parser_for">get_parser_for() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader.get_radii">get_radii() (MDAnalysis.coordinates.PQR.PQRReader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.get_radii">(MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.get_reader_for">get_reader_for() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.get_writer">get_writer() (in module MDAnalysis.selections.base)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.get_writer_for">get_writer_for() (in module MDAnalysis.coordinates.core)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.getconstrain">getconstrain() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.greedy_splitext">greedy_splitext() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid">Grid (class in MDAnalysis.analysis.density)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.group">group() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.groups">groups() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.groups_iter">groups_iter() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dt><a href="documentation_pages/coordinates/GRO.html#MDAnalysis.coordinates.GRO.GROWriter">GROWriter (class in MDAnalysis.coordinates.GRO)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_atom_charge">guess_atom_charge() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_atom_element">guess_atom_element() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_atom_mass">guess_atom_mass() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_atom_type">guess_atom_type() (in module MDAnalysis.topology.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.guess_format">guess_format() (in module MDAnalysis.coordinates.core)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.guess_format">(in module MDAnalysis.topology.core)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="H">H</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.has_valid_coordinates">has_valid_coordinates() (MDAnalysis.coordinates.base.Writer method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.has_valid_coordinates">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.has_valid_coordinates">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/helanal.html#MDAnalysis.analysis.helanal.helanal_main">helanal_main() (in module MDAnalysis.analysis.helanal)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/helanal.html#MDAnalysis.analysis.helanal.helanal_trajectory">helanal_trajectory() (in module MDAnalysis.analysis.helanal)</a></dt>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis">HydrogenBondAnalysis (class in MDAnalysis.analysis.hbonds)</a></dt>
</dl></td>
</tr></table>

<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.improper">improper() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/qcprot.html#MDAnalysis.core.qcprot.InnerProduct">InnerProduct() (in module MDAnalysis.core.qcprot)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.interpolated">interpolated (MDAnalysis.analysis.density.Density attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.interpolated">(MDAnalysis.analysis.density.Grid attribute)</a></dt>
  </dl></dd>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase">IObase (class in MDAnalysis.coordinates.base)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.iterable">iterable() (in module MDAnalysis.core.util)</a></dt>
</dl></td>
</tr></table>

<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.join">join() (in module MDAnalysis.selections.base)</a></dt>
</dl></td>
</tr></table>

<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree">KDTree (class in MDAnalysis.KDTree.KDTree)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/topology/tables.html#MDAnalysis.topology.tables.kv2dict">kv2dict() (in module MDAnalysis.topology.tables)</a></dt>
</dl></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder">LeafletFinder (class in MDAnalysis.analysis.leaflet)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#MDAnalysis.topology.core.Bond.length">length() (MDAnalysis.topology.core.Bond method)</a></dt>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.lengthUnit_factor">lengthUnit_factor (in module MDAnalysis.core.units)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.list_search">list_search() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.load">load() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.load">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.load">(MDAnalysis.analysis.density.Density method)</a></dt>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.load">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.load_new">load_new() (MDAnalysis.core.AtomGroup.Universe method)</a></dt>
</dl></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.make_density">make_density() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dt><a href="documentation_pages/topology/tables.html#MDAnalysis.topology.tables.masses">masses (in module MDAnalysis.topology.tables)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.masses">masses() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.matrix">matrix() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align">MDAnalysis.analysis.align (module)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#module-MDAnalysis.analysis.contacts">MDAnalysis.analysis.contacts (module)</a></dt>
    <dt><a href="documentation_pages/analysis/density.html#module-MDAnalysis.analysis.density">MDAnalysis.analysis.density (module)</a></dt>
    <dt><a href="documentation_pages/analysis/distances.html#module-MDAnalysis.analysis.distances">MDAnalysis.analysis.distances (module)</a></dt>
    <dt><a href="documentation_pages/analysis/hbonds.html#module-MDAnalysis.analysis.hbonds">MDAnalysis.analysis.hbonds (module)</a></dt>
    <dt><a href="documentation_pages/analysis/helanal.html#module-MDAnalysis.analysis.helanal">MDAnalysis.analysis.helanal (module)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#module-MDAnalysis.analysis.leaflet">MDAnalysis.analysis.leaflet (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/init.html#module-MDAnalysis.coordinates.__init__">MDAnalysis.coordinates.__init__ (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#module-MDAnalysis.coordinates.base">MDAnalysis.coordinates.base (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#module-MDAnalysis.coordinates.core">MDAnalysis.coordinates.core (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/CRD.html#module-MDAnalysis.coordinates.CRD">MDAnalysis.coordinates.CRD (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/DCD.html#module-MDAnalysis.coordinates.DCD">MDAnalysis.coordinates.DCD (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/GRO.html#module-MDAnalysis.coordinates.GRO">MDAnalysis.coordinates.GRO (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#module-MDAnalysis.coordinates.PDB">MDAnalysis.coordinates.PDB (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDBQT.html#module-MDAnalysis.coordinates.PDBQT">MDAnalysis.coordinates.PDBQT (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/PQR.html#module-MDAnalysis.coordinates.PQR">MDAnalysis.coordinates.PQR (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRJ.html#module-MDAnalysis.coordinates.TRJ">MDAnalysis.coordinates.TRJ (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#module-MDAnalysis.coordinates.TRR">MDAnalysis.coordinates.TRR (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#module-MDAnalysis.coordinates.xdrfile.libxdrfile">MDAnalysis.coordinates.xdrfile.libxdrfile (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#module-MDAnalysis.coordinates.xdrfile.TRR">MDAnalysis.coordinates.xdrfile.TRR (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/XTC.html#module-MDAnalysis.coordinates.xdrfile.XTC">MDAnalysis.coordinates.xdrfile.XTC (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/XTC.html#module-MDAnalysis.coordinates.XTC">MDAnalysis.coordinates.XTC (module)</a></dt>
    <dt><a href="documentation_pages/coordinates/XYZ.html#module-MDAnalysis.coordinates.XYZ">MDAnalysis.coordinates.XYZ (module)</a></dt>
    <dt><a href="documentation_pages/core/init.html#module-MDAnalysis.core.__init__">MDAnalysis.core.__init__ (module)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup">MDAnalysis.core.AtomGroup (module)</a></dt>
    <dt><a href="documentation_pages/core/distances.html#module-MDAnalysis.core.distances">MDAnalysis.core.distances (module)</a></dt>
    <dt><a href="documentation_pages/core/log.html#module-MDAnalysis.core.log">MDAnalysis.core.log (module)</a></dt>
    <dt><a href="documentation_pages/core/qcprot.html#module-MDAnalysis.core.qcprot">MDAnalysis.core.qcprot (module)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#module-MDAnalysis.core.Selection">MDAnalysis.core.Selection (module)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#module-MDAnalysis.core.Timeseries">MDAnalysis.core.Timeseries (module)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#module-MDAnalysis.core.transformations">MDAnalysis.core.transformations (module)</a></dt>
    <dt><a href="documentation_pages/core/units.html#module-MDAnalysis.core.units">MDAnalysis.core.units (module)</a></dt>
    <dt><a href="documentation_pages/core/util.html#module-MDAnalysis.core.util">MDAnalysis.core.util (module)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#module-MDAnalysis.KDTree.KDTree">MDAnalysis.KDTree.KDTree (module)</a></dt>
    <dt><a href="documentation_pages/KDTree/NeighborSearch.html#module-MDAnalysis.KDTree.NeighborSearch">MDAnalysis.KDTree.NeighborSearch (module)</a></dt>
    <dt><a href="documentation_pages/selections/base.html#module-MDAnalysis.selections.base">MDAnalysis.selections.base (module)</a></dt>
    <dt><a href="documentation_pages/selections/charmm.html#module-MDAnalysis.selections.charmm">MDAnalysis.selections.charmm (module)</a></dt>
    <dt><a href="documentation_pages/selections/gromacs.html#module-MDAnalysis.selections.gromacs">MDAnalysis.selections.gromacs (module)</a></dt>
    <dt><a href="documentation_pages/selections/pymol.html#module-MDAnalysis.selections.pymol">MDAnalysis.selections.pymol (module)</a></dt>
    <dt><a href="documentation_pages/selections/vmd.html#module-MDAnalysis.selections.vmd">MDAnalysis.selections.vmd (module)</a></dt>
    <dt><a href="documentation_pages/topology/init.html#module-MDAnalysis.topology.__init__">MDAnalysis.topology.__init__ (module)</a></dt>
    <dt><a href="documentation_pages/topology/core.html#module-MDAnalysis.topology.core">MDAnalysis.topology.core (module)</a></dt>
    <dt><a href="documentation_pages/topology/CRDParser.html#module-MDAnalysis.topology.CRDParser">MDAnalysis.topology.CRDParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/GROParser.html#module-MDAnalysis.topology.GROParser">MDAnalysis.topology.GROParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/PDBParser.html#module-MDAnalysis.topology.PDBParser">MDAnalysis.topology.PDBParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/PDBQTParser.html#module-MDAnalysis.topology.PDBQTParser">MDAnalysis.topology.PDBQTParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/PQRParser.html#module-MDAnalysis.topology.PQRParser">MDAnalysis.topology.PQRParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/PrimitivePDBParser.html#module-MDAnalysis.topology.PrimitivePDBParser">MDAnalysis.topology.PrimitivePDBParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/PSFParser.html#module-MDAnalysis.topology.PSFParser">MDAnalysis.topology.PSFParser (module)</a></dt>
    <dt><a href="documentation_pages/topology/tables.html#module-MDAnalysis.topology.tables">MDAnalysis.topology.tables (module)</a></dt>
    <dt><a href="documentation_pages/topology/TOPParser.html#module-MDAnalysis.topology.TOPParser">MDAnalysis.topology.TOPParser (module)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.momentOfInertia">momentOfInertia() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
</dl></td>
</tr></table>

<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.N_Avogadro">N_Avogadro (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.names">names() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.next">next() (MDAnalysis.coordinates.base.Reader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.next">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.next">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
      <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.next">(MDAnalysis.core.transformations.Arcball method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.norm">norm() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.normal">normal() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.NucleicBackboneSelection">NucleicBackboneSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.NucleicSelection">NucleicSelection (class in MDAnalysis.core.Selection)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.NucleicSugarSelection">NucleicSugarSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.NucleicXstalSelection">NucleicXstalSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.NullHandler">NullHandler (class in MDAnalysis.core.log)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.numatoms">numatoms (MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/XYZ.html#MDAnalysis.coordinates.XYZ.XYZReader.numatoms">(MDAnalysis.coordinates.XYZ.XYZReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.numatoms">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.FORTRANReader.number_of_matches">number_of_matches() (MDAnalysis.core.util.FORTRANReader method)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader.numframes">numframes (MDAnalysis.coordinates.TRJ.TRJReader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.numframes">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.numframes">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader.open_trajectory">open_trajectory() (MDAnalysis.coordinates.TRJ.TRJReader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.open_trajectory">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.open_trajectory">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.openany">openany() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.optimize_cutoff">optimize_cutoff() (in module MDAnalysis.analysis.leaflet)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.OtherWriter">OtherWriter() (MDAnalysis.coordinates.base.Reader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.OtherWriter">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.OtherWriter">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.output_exists">output_exists() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.output_exists">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/topology/CRDParser.html#MDAnalysis.topology.CRDParser.parse">parse() (in module MDAnalysis.topology.CRDParser)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/topology/GROParser.html#MDAnalysis.topology.GROParser.parse">(in module MDAnalysis.topology.GROParser)</a></dt>
      <dt><a href="documentation_pages/topology/PDBParser.html#MDAnalysis.topology.PDBParser.parse">(in module MDAnalysis.topology.PDBParser)</a></dt>
      <dt><a href="documentation_pages/topology/PDBQTParser.html#MDAnalysis.topology.PDBQTParser.parse">(in module MDAnalysis.topology.PDBQTParser)</a></dt>
      <dt><a href="documentation_pages/topology/PQRParser.html#MDAnalysis.topology.PQRParser.parse">(in module MDAnalysis.topology.PQRParser)</a></dt>
      <dt><a href="documentation_pages/topology/PSFParser.html#MDAnalysis.topology.PSFParser.parse">(in module MDAnalysis.topology.PSFParser)</a></dt>
      <dt><a href="documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.PrimitivePDBParser.parse">(in module MDAnalysis.topology.PrimitivePDBParser)</a></dt>
      <dt><a href="documentation_pages/topology/TOPParser.html#MDAnalysis.topology.TOPParser.parse">(in module MDAnalysis.topology.TOPParser)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.FORTRANReader.parse_FORTRAN_format">parse_FORTRAN_format() (MDAnalysis.core.util.FORTRANReader method)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.parse_residue">parse_residue() (in module MDAnalysis.core.util)</a></dt>
    <dt><a href="documentation_pages/topology/PDBParser.html#MDAnalysis.topology.PDBParser.PDBParseError">PDBParseError</a>, <a href="documentation_pages/topology/PrimitivePDBParser.html#MDAnalysis.topology.PrimitivePDBParser.PDBParseError">[1]</a></dt>
    <dt><a href="documentation_pages/topology/PDBQTParser.html#MDAnalysis.topology.PDBQTParser.PDBQTParseError">PDBQTParseError</a></dt>
    <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader">PDBQTReader (class in MDAnalysis.coordinates.PDBQT)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter">PDBQTWriter (class in MDAnalysis.coordinates.PDBQT)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PDBReader">PDBReader (class in MDAnalysis.coordinates.PDB)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PDBWriter">PDBWriter (class in MDAnalysis.coordinates.PDB)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.place">place() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.plot">plot() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.plot">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.plot_qavg">plot_qavg() (MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.pos">pos (MDAnalysis.core.AtomGroup.Atom attribute)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/PQR.html#MDAnalysis.coordinates.PQR.PQRReader">PQRReader (class in MDAnalysis.coordinates.PQR)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader">PrimitivePDBReader (class in MDAnalysis.coordinates.PDB)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter">PrimitivePDBWriter (class in MDAnalysis.coordinates.PDB)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.principalAxes">principalAxes() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.PrincipleAxis">PrincipleAxis (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.ProgressMeter">ProgressMeter (class in MDAnalysis.core.log)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.projection_from_matrix">projection_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flag.prop">prop() (MDAnalysis.core.__init__.Flag method)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.PropertySelection">PropertySelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.ProteinSelection.prot_res">prot_res (MDAnalysis.core.Selection.ProteinSelection attribute)</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.ProteinSelection">ProteinSelection (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/topology/PSFParser.html#MDAnalysis.topology.PSFParser.PSFParseError">PSFParseError</a></dt>
</dl></td>
</tr></table>

<h2 id="Q">Q</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.qarray">qarray() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.qarray">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.qN">qN() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.qN">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
  </dl></dd>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.quaternion_imag">quaternion_imag() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.quaternion_real">quaternion_real() (in module MDAnalysis.core.transformations)</a></dt>
</dl></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radii">radii() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.radiusOfGyration">radiusOfGyration() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.FORTRANReader.read">read() (MDAnalysis.core.util.FORTRANReader method)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_trr">read_trr() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_trr_natoms">read_trr_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_trr_numframes">read_trr_numframes() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_xtc">read_xtc() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_xtc_natoms">read_xtc_natoms() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.read_xtc_numframes">read_xtc_numframes() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader">Reader (class in MDAnalysis.coordinates.base)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.reader">reader() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.reflection_from_matrix">reflection_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flags.register">register() (MDAnalysis.core.__init__.Flags method)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.REMARK">REMARK() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter.REMARK">(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.resample">resample() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.resample">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.resample_factor">resample_factor() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.resample_factor">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resids">resids() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Residue">Residue (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.ResidueGroup">ResidueGroup (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.residues">residues (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resnames">resnames() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.resnums">resnums() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.rewind">rewind() (MDAnalysis.coordinates.base.ChainReader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader.rewind">(MDAnalysis.coordinates.TRJ.TRJReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XYZ.html#MDAnalysis.coordinates.XYZ.XYZReader.rewind">(MDAnalysis.coordinates.XYZ.XYZReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.rewind">(MDAnalysis.coordinates.base.Reader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.rewind">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.rewind">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.rms_fit_trj">rms_fit_trj() (in module MDAnalysis.analysis.align)</a></dt>
    <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.rmsd">rmsd() (in module MDAnalysis.analysis.align)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.rotate">rotate() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.rotateby">rotateby() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.rotation_from_matrix">rotation_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/analysis/align.html#MDAnalysis.analysis.align.rotation_matrix">rotation_matrix() (in module MDAnalysis.analysis.align)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.rotaxis">rotaxis() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis.run">run() (MDAnalysis.analysis.contacts.ContactAnalysis method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/contacts.html#MDAnalysis.analysis.contacts.ContactAnalysis1.run">(MDAnalysis.analysis.contacts.ContactAnalysis1 method)</a></dt>
      <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.run">(MDAnalysis.analysis.hbonds.HydrogenBondAnalysis method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Density.save">save() (MDAnalysis.analysis.density.Density method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/analysis/density.html#MDAnalysis.analysis.density.Grid.save">(MDAnalysis.analysis.density.Grid method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/hbonds.html#MDAnalysis.analysis.hbonds.HydrogenBondAnalysis.save_table">save_table() (MDAnalysis.analysis.hbonds.HydrogenBondAnalysis method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.scale_from_matrix">scale_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.search">search() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch.search">(MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method)</a></dt>
      <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch.search">(MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch.search_all">search_all() (MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch.search_all">(MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch.search_list">search_list() (MDAnalysis.KDTree.NeighborSearch.AtomNeighborSearch method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/KDTree/NeighborSearch.html#MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch.search_list">(MDAnalysis.KDTree.NeighborSearch.CoordinateNeighborSearch method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.segids">segids() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Segment">Segment (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SegmentGroup">SegmentGroup (class in MDAnalysis.core.AtomGroup)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.segments">segments (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.selectAtoms">selectAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.selectAtoms">(MDAnalysis.core.AtomGroup.Universe method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionError">SelectionError</a></dt>
    <dt><a href="documentation_pages/core/Selection.html#MDAnalysis.core.Selection.SelectionParser">SelectionParser (class in MDAnalysis.core.Selection)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.SelectionWarning">SelectionWarning</a></dt>
    <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter">SelectionWriter (class in MDAnalysis.selections.base)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/selections/charmm.html#MDAnalysis.selections.charmm.SelectionWriter">(class in MDAnalysis.selections.charmm)</a></dt>
      <dt><a href="documentation_pages/selections/gromacs.html#MDAnalysis.selections.gromacs.SelectionWriter">(class in MDAnalysis.selections.gromacs)</a></dt>
      <dt><a href="documentation_pages/selections/pymol.html#MDAnalysis.selections.pymol.SelectionWriter">(class in MDAnalysis.selections.pymol)</a></dt>
      <dt><a href="documentation_pages/selections/vmd.html#MDAnalysis.selections.vmd.SelectionWriter">(class in MDAnalysis.selections.vmd)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/distances.html#MDAnalysis.analysis.distances.self_distance_array">self_distance_array() (in module MDAnalysis.analysis.distances)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/distances.html#MDAnalysis.core.distances.self_distance_array">(in module MDAnalysis.core.distances)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_bfactor">set_bfactor() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_charge">set_charge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/KDTree/KDTree.html#MDAnalysis.KDTree.KDTree.KDTree.set_coords">set_coords() (MDAnalysis.KDTree.KDTree.KDTree method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_mass">set_mass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_name">set_name() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_radius">set_radius() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resid">set_resid() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resname">set_resname() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_resnum">set_resnum() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_segid">set_segid() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.set_type">set_type() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.setaxes">setaxes() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.Arcball.setconstrain">setconstrain() (MDAnalysis.core.transformations.Arcball method)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Timeseries.shape">shape (MDAnalysis.core.Timeseries.Timeseries attribute)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.shear_from_matrix">shear_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.sizes">sizes() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.start_logging">start_logging() (in module MDAnalysis)</a></dt>
    <dt><a href="documentation_pages/core/log.html#MDAnalysis.stop_logging">stop_logging() (in module MDAnalysis)</a></dt>
    <dt><a href="documentation_pages/core/util.html#MDAnalysis.core.util.stp">stp() (in module MDAnalysis.core.util)</a></dt>
</dl></td>
</tr></table>

<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/topology/tables.html#MDAnalysis.topology.tables.TABLE_ATOMELEMENTS">TABLE_ATOMELEMENTS (in module MDAnalysis.topology.tables)</a></dt>
    <dt><a href="documentation_pages/topology/tables.html#MDAnalysis.topology.tables.TABLE_MASSES">TABLE_MASSES (in module MDAnalysis.topology.tables)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ChainReader.time">time (MDAnalysis.coordinates.base.ChainReader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.time">(MDAnalysis.coordinates.base.Reader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.time">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.time">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.Timeseries">Timeseries (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.timeseries">timeseries() (MDAnalysis.coordinates.DCD.DCDReader method)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.TimeseriesCollection">TimeseriesCollection (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep">Timestep (class in MDAnalysis.coordinates.base)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.Timestep">(class in MDAnalysis.coordinates.TRJ)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep">(class in MDAnalysis.coordinates.xdrfile.TRR)</a>, <a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep">[1]</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep">(class in MDAnalysis.coordinates.xdrfile.XTC)</a>, <a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep">[1]</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.timeUnit_factor">timeUnit_factor (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.TITLE">TITLE() (MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter.TITLE">(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/topology/TOPParser.html#MDAnalysis.topology.TOPParser.TOPParseError">TOPParseError</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalCharge">totalCharge() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.totalMass">totalMass() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.totaltime">totaltime (MDAnalysis.coordinates.base.Reader attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.totaltime">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.totaltime">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe.trajectory">trajectory (MDAnalysis.core.AtomGroup.Universe attribute)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.transform">transform() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.translate">translate() (MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.translation_from_matrix">translation_from_matrix() (in module MDAnalysis.core.transformations)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.triclinic_box">triclinic_box() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.triclinic_vectors">triclinic_vectors() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRJ.html#MDAnalysis.coordinates.TRJ.TRJReader">TRJReader (class in MDAnalysis.coordinates.TRJ)</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader">TRRReader (class in MDAnalysis.coordinates.xdrfile.TRR)</a>, <a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader">[1]</a></dt>
    <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter">TRRWriter (class in MDAnalysis.coordinates.xdrfile.TRR)</a>, <a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter">[1]</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.ts">ts (MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
</dl></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.unit_types">unit_types (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.IObase.units">units (MDAnalysis.coordinates.base.IObase attribute)</a></dt>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Universe">Universe (class in MDAnalysis.core.AtomGroup)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.Atom.universe">universe (MDAnalysis.core.AtomGroup.Atom attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.universe">(MDAnalysis.core.AtomGroup.AtomGroup attribute)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.update">update() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/init.html#MDAnalysis.core.__init__.Flags.update">(MDAnalysis.core.__init__.Flags method)</a></dt>
      <dt><a href="documentation_pages/core/log.html#MDAnalysis.core.log.ProgressMeter.update">(MDAnalysis.core.log.ProgressMeter method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/transformations.html#MDAnalysis.core.transformations.vecangle">vecangle() (in module MDAnalysis.core.transformations)</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Timestep.volume">volume (MDAnalysis.coordinates.base.Timestep attribute)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.Timestep.volume">(MDAnalysis.coordinates.xdrfile.TRR.Timestep attribute)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.Timestep.volume">(MDAnalysis.coordinates.xdrfile.XTC.Timestep attribute)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="W">W</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/core/units.html#MDAnalysis.core.units.water">water (in module MDAnalysis.core.units)</a></dt>
    <dt><a href="documentation_pages/core/Timeseries.html#MDAnalysis.core.Timeseries.WaterDipole">WaterDipole (class in MDAnalysis.core.Timeseries)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer.write">write() (MDAnalysis.coordinates.base.Writer method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/CRD.html#MDAnalysis.coordinates.CRD.CRDWriter.write">(MDAnalysis.coordinates.CRD.CRDWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/GRO.html#MDAnalysis.coordinates.GRO.GROWriter.write">(MDAnalysis.coordinates.GRO.GROWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PDBWriter.write">(MDAnalysis.coordinates.PDB.PDBWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBWriter.write">(MDAnalysis.coordinates.PDB.PrimitivePDBWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTWriter.write">(MDAnalysis.coordinates.PDBQT.PDBQTWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write">(MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
      <dt><a href="documentation_pages/selections/base.html#MDAnalysis.selections.base.SelectionWriter.write">(MDAnalysis.selections.base.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/charmm.html#MDAnalysis.selections.charmm.SelectionWriter.write">(MDAnalysis.selections.charmm.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/gromacs.html#MDAnalysis.selections.gromacs.SelectionWriter.write">(MDAnalysis.selections.gromacs.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/pymol.html#MDAnalysis.selections.pymol.SelectionWriter.write">(MDAnalysis.selections.pymol.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/vmd.html#MDAnalysis.selections.vmd.SelectionWriter.write">(MDAnalysis.selections.vmd.SelectionWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDWriter.write_next_timestep">write_next_timestep() (MDAnalysis.coordinates.DCD.DCDWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRWriter.write_next_timestep">(MDAnalysis.coordinates.xdrfile.TRR.TRRWriter method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter.write_next_timestep">(MDAnalysis.coordinates.xdrfile.XTC.XTCWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/selections/charmm.html#MDAnalysis.selections.charmm.SelectionWriter.write_preamble">write_preamble() (MDAnalysis.selections.charmm.SelectionWriter method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/selections/gromacs.html#MDAnalysis.selections.gromacs.SelectionWriter.write_preamble">(MDAnalysis.selections.gromacs.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/pymol.html#MDAnalysis.selections.pymol.SelectionWriter.write_preamble">(MDAnalysis.selections.pymol.SelectionWriter method)</a></dt>
      <dt><a href="documentation_pages/selections/vmd.html#MDAnalysis.selections.vmd.SelectionWriter.write_preamble">(MDAnalysis.selections.vmd.SelectionWriter method)</a></dt>
  </dl></dd>
    <dt><a href="documentation_pages/analysis/leaflet.html#MDAnalysis.analysis.leaflet.LeafletFinder.write_selection">write_selection() (MDAnalysis.analysis.leaflet.LeafletFinder method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/core/AtomGroup.html#MDAnalysis.core.AtomGroup.AtomGroup.write_selection">(MDAnalysis.core.AtomGroup.AtomGroup method)</a></dt>
  </dl></dd>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.write_trr">write_trr() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.write_xtc">write_xtc() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Writer">Writer (class in MDAnalysis.coordinates.base)</a></dt>
    <dt><a href="documentation_pages/coordinates/core.html#MDAnalysis.coordinates.core.writer">writer() (in module MDAnalysis.coordinates.core)</a></dt>
    <dt><a href="documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.Reader.Writer">Writer() (MDAnalysis.coordinates.base.Reader method)</a></dt>
    <dd><dl>
      <dt><a href="documentation_pages/coordinates/CRD.html#MDAnalysis.coordinates.CRD.CRDReader.Writer">(MDAnalysis.coordinates.CRD.CRDReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/DCD.html#MDAnalysis.coordinates.DCD.DCDReader.Writer">(MDAnalysis.coordinates.DCD.DCDReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PDBReader.Writer">(MDAnalysis.coordinates.PDB.PDBReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDB.html#MDAnalysis.coordinates.PDB.PrimitivePDBReader.Writer">(MDAnalysis.coordinates.PDB.PrimitivePDBReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/PDBQT.html#MDAnalysis.coordinates.PDBQT.PDBQTReader.Writer">(MDAnalysis.coordinates.PDBQT.PDBQTReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/TRR.html#MDAnalysis.coordinates.xdrfile.TRR.TRRReader.Writer">(MDAnalysis.coordinates.xdrfile.TRR.TRRReader method)</a></dt>
      <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader.Writer">(MDAnalysis.coordinates.xdrfile.XTC.XTCReader method)</a></dt>
  </dl></dd>
</dl></td>
</tr></table>

<h2 id="X">X</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.xdrfile_close">xdrfile_close() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/libxdrfile.html#MDAnalysis.coordinates.xdrfile.libxdrfile.xdrfile_open">xdrfile_open() (in module MDAnalysis.coordinates.xdrfile.libxdrfile)</a></dt>
    <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader">XTCReader (class in MDAnalysis.coordinates.xdrfile.XTC)</a>, <a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCReader">[1]</a></dt>
</dl></td>
  <td style="width: 33%" valign="top"><dl>
    <dt><a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter">XTCWriter (class in MDAnalysis.coordinates.xdrfile.XTC)</a>, <a href="documentation_pages/coordinates/XTC.html#MDAnalysis.coordinates.xdrfile.XTC.XTCWriter">[1]</a></dt>
    <dt><a href="documentation_pages/coordinates/XYZ.html#MDAnalysis.coordinates.XYZ.XYZReader">XYZReader (class in MDAnalysis.coordinates.XYZ)</a></dt>
</dl></td>
</tr></table>



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